66 Works

Data from: Evolutionary history of the angiosperm flora of China

Li-Min Lu, Ling-Feng Mao, Tuo Yang, Jian-Fei Ye, Bing Liu, Hong-Lei Li, Miao Sun, Joseph T. Miller, Sarah Mathews, Hai-Hua Hu, Yan-Ting Niu, Dan-Xiao Peng, You-Hua Chen, Stephen A. Smith, Min Chen, Kun-Li Xiang, Chi-Toan Le, Viet-Cuong Dang, An-Ming Lu, Pamela S. Soltis, Douglas E. Soltis, Jian-Hua Li & Zhi-Duan Chen
High species diversity may result from recent rapid speciation in a ‘cradle’ and/or the gradual accumulation and preservation of species over time in a ‘museum’1,2. China harbours nearly 10% of angiosperm species worldwide and has long been considered as both a museum, owing to the presence of many species with hypothesized ancient origins3,4, and a cradle, as many lineages have originated as recent topographic changes and climatic shifts—such as the formation of the Qinghai–Tibetan Plateau...

Data from: Age‐dependent leaf physiology and consequences for crown‐scale carbon uptake during the dry season in an Amazon evergreen forest

Loren P. Albert, Jin Wu, Neill Prohaska, Plinio Barbosa De Camargo, Travis E. Huxman, Edgard S. Tribuzy, Valeriy Y. Ivanov, Rafael S. Oliveira, Sabrina Garcia, Marielle N. Smith, Raimundo Cosme Oliveira Junior, Natalia Restrepo-Coupe, Rodrigo Da Silva, Scott C. Stark, Giordane A. Martins, Deliane V. Penha & Scott R. Saleska
* Satellite and tower-based metrics of forest-scale photosynthesis generally increase with dry season progression across central Amazônia, but the underlying mechanisms lack consensus. * We conducted demographic surveys of leaf age composition, and measured age-dependence of leaf physiology in broadleaf canopy trees of abundant species at a central eastern Amazon site. Using a novel leaf-to-branch scaling approach, we used this data to independently test the much-debated hypothesis—arising from satellite and tower-based observations—that leaf phenology could...

Data from: An inverse latitudinal gradient in speciation rate for marine fishes

Daniel L. Rabosky, Jonathan Chang, Pascal O. Title, Peter F. Cowman, Lauren Sallan, Matt Friedman, Kristin Kaschner, Cristina Garilao, Thomas J. Near, Marta Coll & Michael E. Alfaro
Far more species of organisms are found in the tropics than in temperate and polar regions, but the evolutionary and ecological causes of this pattern remain controversial1,2. Tropical marine fish communities are much more diverse than cold-water fish communities found at higher latitudes3,4, and several explanations for this latitudinal diversity gradient propose that warm reef environments serve as evolutionary ‘hotspots’ for species formation5,6,7,8. Here we test the relationship between latitude, species richness and speciation rate...

Data from: Within-host priority effects systematically alter pathogen coexistence

Patrick A. Clay, Kailash Dhir, Volker H.W. Rudolf, Meghan A. Duffy & Volker H. W. Rudolf
Coinfection of host populations alters pathogen prevalence, host mortality, and pathogen evolution. Because pathogens compete for limiting resources, whether multiple pathogens can coexist in a host population can depend on their within-host interactions which, in turn, can depend on the order in which pathogens infect hosts (within-host priority effects). However, the consequences of within-host priority effects for pathogen coexistence have not been tested. Using laboratory studies with a coinfected zooplankton system, we found that pathogens...

Data from: Vegetation connectivity increases ant activity and potential for ant-provided biocontrol services in a tropical agroforest

Estelí Jimenez-Soto, Jonathan R. Morris, Deborah K. Letourneau, Stacy M. Philpott. & Stacy M. Philpott
In natural and managed systems, connections between trees are important structural resources for arboreal ant communities with ecosystem-level effects. However, ongoing agricultural intensification in agroforestry systems, which reduces shade trees and connectivity between trees and crop plants, may hinder ant recruitment rates to resources and pest control services provided by ants. We examined whether increasing connectivity between coffee plants and shade trees in coffee plantations increases ant activity and enhances biological control of the coffee...

Data from: Digitizing extant bat diversity: an open-access repository of 3D μCT-scanned skulls for research and education

Jeff J. Shi, Erin P. Westeen & Daniel L. Rabosky
Biological specimens are primary records of organismal ecology and history. As such, museum collections are invaluable repositories for testing ecological and evolutionary hypotheses across the tree of life. Digitizing and broadly sharing the phenotypic data from these collections serves to expand the traditional reach of museums, enabling widespread data sharing, collaboration, and education at an unprecedented scale. In recent years, μCT-scanning has been adopted as one way for efficiently digitizing museum specimens. Here, we describe...

Data from: Evaluating a handheld decision support device in pediatric intensive care settings

Tera L. Reynolds, Patricia R. DeLucia, Karen A. Esquibel, Todd Gage, Noah J. Wheeler, J. Adam Randell, James G. Stevenson & Kai Zheng
Objective: To evaluate end-user acceptance and the effect of a commercial handheld decision support device in pediatric intensive care settings. The technology, pac2, was designed to assist nurses in calculating medication dose volumes and infusion rates at the bedside. Materials and Methods: The devices, manufactured by InformMed Inc., were deployed in the pediatric and neonatal intensive care units in two health systems. This mixed methods study assessed end-user acceptance, as well as pac2’s effect on...

Data from: Hydrological niche segregation defines forest structure and drought tolerance strategies in a seasonal Amazon forest

Mauro Brum, Matthew A. Vadeboncoeur, Valeriy Ivanov, Heidi Asbjornsen, Scott Saleska, Luciana F. Alves, Deliane Penha, Jadson D. Dias, Luiz E.O.C. Aragão, Fernanda Barros, Paulo Bittencourt, Luciano Pereira & Rafael S. Oliveira
1) Understanding if and how trees coordinate rooting depth and aboveground hydraulic traits to define drought-resistance strategies in seasonal Amazon forests is a major gap to model parametrization aimed at predicting the effects of climate change in these ecosystems. 2) We assessed the rooting depth of 12 dominant tree species (representing ~ 42% of the forest basal area) in a seasonal Amazon forest, using the stable isotope ratios (δ18O and δ²H) of water collected from...

Data from: Analyzing contentious relationships and outlier genes in phylogenomics

Joseph F. Walker, Joseph W. Brown & Stephen A. Smith
Recent studies have demonstrated that conflict is common among gene trees in phylogenomic studies, and that less than one percent of genes may ultimately drive species tree inference in supermatrix analyses. Here, we examined two datasets where supermatrix and coalescent-based species trees conflict. We identified two highly influential “outlier” genes in each dataset. When removed from each dataset, the inferred supermatrix trees matched the topologies obtained from coalescent analyses. We also demonstrate that, while the...

Data from: Stress in biological invasions: introduced invasive grey squirrels increase physiological stress in native Eurasian red squirrels

Francesca Santicchia, Ben Dantzer, Freya Van Kesteren, Rupert Palme, Adriano Martinoli, Nicola Ferrari & Lucas Armand Wauters
1. Invasive alien species can cause extinction of native species through processes including predation, interspecific competition for resources, or disease-mediated competition. Increases in stress hormones in vertebrates may be associated with these processes and contribute to the decline in survival or reproduction of the native species. 2. Eurasian red squirrels (Sciurus vulgaris) have gone extinct across much of the British Isles and parts of Northern Italy following the introduction of North American invasive grey squirrels...

Data from: Phytochemical changes in milkweed induced by elevated CO2 alter wing morphology but not toxin sequestration in monarch butterflies

Leslie E. Decker, Abrianna J. Soule, Jacobus C. De Roode & Mark D. Hunter
1. Environmental change has the potential to influence trophic interactions by altering the defensive phenotype of prey. 2. Here, we examine the effects of a pervasive environmental change driver, elevated atmospheric concentrations of CO2 (eCO2), on toxin sequestration and flight morphology of a specialist herbivore. 3. We fed monarch butterfly larvae, Danaus plexippus, foliage from four milkweed, Asclepias, species of varying chemical defense profiles grown under either ambient or eCO2. We also infected a subset...

Data from: Multiple forms of selection shape reproductive isolation in a primate hybrid zone

Marcella D. Baiz, Priscilla K. Tucker & Liliana Cortés-Ortiz
Speciation occurs when populations diverge and become reproductively isolated from each other. Natural selection is commonly accepted to play a large role in this process and it has been widely assumed that reproductive isolation often results as a byproduct of divergence driven by adaptation in allopatry. When such populations come into secondary contact, reinforcement can act to strengthen reproductive isolation, but the frequency and importance of this process is still unknown. Here, we explored genomic...

Data from: Evolution of the latitudinal gradient in the hyperdiverse ant genus Pheidole

Evan P. Economo, Jen-Pan Huang, Georg Fischer, Eli M. Sarnat, Nitish Narula, Milan Janda, Benoit Guénard, John T. Longino & L. Lacey Knowles
Aim: The latitudinal diversity gradient is the dominant pattern of life on Earth, but a consensus understanding of its origins has remained elusive. The analysis of recently diverged, hyper-rich invertebrate groups provides an opportunity to investigate latitudinal patterns with the statistical power of large trees while minimizing potentially confounding variation in ecology and history. Here, we synthesize global phylogenetic and macroecological data on a hyperdiverse (>1100 species) ant radiation, Pheidole, and test predictions of three...

Data from: Phylogenies and diversification rates: variance cannot be ignored

Daniel L Rabosky
A recent pair of articles published in the journal Evolution presented a test for assessing the validity of hierarchical macroevolutionary models. The premise of the test is to compare numerical point estimates of parameters from two levels of analysis; if the estimates differ, the hierarchical model is purportedly flawed. The articles in question (Meyer and Wiens 2017; Meyer et al. 2018) apply their proposed test to BAMM, a scientific software program that uses a Bayesian...

Data from: Social and ecological drivers of reproductive seasonality in geladas

Elizabeth Tinsley Johnson, Noah Snyder-Mackler, Amy Lu, Thore J. Bergman & Jacinta C. Beehner
Many non-seasonally breeding mammals demonstrate some degree of synchrony in births, which is generally associated with ecological factors that mediate fecundity. However, disruptive social events, such as alpha male replacements, also have the potential to affect the timing of female reproduction. Here, we examined reproductive seasonality in a wild population of geladas (Theropithecus gelada) living at high altitudes in an afro-alpine ecosystem in Ethiopia. Using 9 years of demographic data (2006-2014) we determined that, while...

Data from: Empty conformers of HLA-B preferentially bind CD8 and regulate CD8+ T cell function

Jie Geng, John D. Altman, Sujatha Krishnakumar & Malini Raghavan
When complexed with antigenic peptides, human leukocyte antigen (HLA) class I (HLA-I) molecules initiate CD8+ T cell responses via interaction with the T cell receptor (TCR) and co-receptor CD8. Peptides are generally critical for the stable cell surface expression of HLA-I molecules. However, for HLA-I alleles such as HLA-B35:01, peptide-deficient (empty) heterodimers are thermostable and detectable on the cell surface. Additionally, peptide-deficient HLA-B35:01 tetramers preferentially bind CD8 and to a majority of blood-derived CD8+ T...

Data from: The global geography of human subsistence

Michael C. Gavin, Patrick H. Kavanagh, Hannah J. Haynie, Claire Bowern, Carol R. Ember, Russell D. Gray, Fiona M. Jordan, Kathryn R. Kirby, Geoff Kushnick, Bobbi S. Low, Bruno Vilela & Carlos A. Botero
How humans obtain food has dramatically reshaped ecosystems and altered both the trajectory of human history and the characteristics of human societies. Our species’ subsistence varies widely, from predominantly foraging strategies, to plant-based agriculture and animal husbandry. The extent to which environmental, social, and historical factors have driven such variation is currently unclear. Prior attempts to resolve long-standing debates on this topic have been hampered by an over-reliance on narrative arguments, small and geographically-narrow samples,...

Data from: Mycorrhizae alter toxin sequestration and performance of two specialist herbivores

Amanda R. Meier & Mark D. Hunter
Multitrophic species interactions are shaped by both top-down and bottom-up factors. Belowground symbionts of plants, such as arbuscular mycorrhizal fungi (AMF), can alter the strength of these forces by altering plant phenotype. For example, AMF-mediated changes in foliar toxin and nutrient concentrations may influence herbivore growth and fecundity. In addition, many specialist herbivores sequester toxins from their host plants to resist natural enemies, and the extent of sequestration varies with host plant secondary chemistry. Therefore,...

Data from: Filter-dispersal assembly of lowland Neotropical rainforests across the Andes

Jordan B. Bemmels, S. Joseph Wright, Nancy C. Garwood, Simon A. Queenborough, Renato Valencia & Christopher W. Dick
Numerous Neotropical rainforest species are distributed in both Amazonia and Central America, reflecting a rich history of biotic interchange between regions. However, some plant lineages are endemic to one region, due in part to the dispersal barrier posed by the northern Andean cordilleras and adjacent savannas. To investigate the role of biogeographic filtering across the northern Andes in regional community assembly, we examined environmental tolerances, functional traits, and biogeographic distributions of >1000 woody plant species...

Data from: Microevolutionary processes impact macroevolutionary patterns

Jingchun Li, Jen-Pen Huang, Jeet Sukumaran & L Lacey Knowles
Background: Macroevolutionary modeling of species diversification plays important roles in inferring large-scale biodiversity patterns. It allows estimation of speciation and extinction rates and statistically testing their relationships with different ecological factors. However, macroevolutionary patterns are ultimately generated by microevolutionary processes acting at population levels, especially when speciation and extinction are considered protracted instead of point events. Neglecting the connection between micro- and macroevolution may hinder our ability to fully understand the underlying mechanisms that drive...

Data from: Selected HLA-B allotypes are resistant to inhibition or deficiency of the transporter associated with antigen processing (TAP)

Jie Geng, Anita Zaitouna, Malini Raghavan & Anita J. Zaitouna
Major histocompatibility complex class I (MHC-I) molecules present antigenic peptides to CD8+ T cells, and are also important for natural killer (NK) cell immune surveillance against infections and cancers. MHC-I molecules are assembled via a complex assembly pathway in the endoplasmic reticulum (ER) of cells. Peptides present in the cytosol of cells are transported into the ER via the transporter associated with antigen processing (TAP). In the ER, peptides are assembled with MHC-I molecules via...

Data from: Ecomorphological and phylogenetic controls on sympatry across extant bats

Jeff J. Shi, Erin P. Westeen, Nathan T. Katlein, Elizabeth R. Dumont & Daniel L. Rabosky
Aim: Macroecological patterns of sympatry can inform our understanding of how ecological and evolutionary processes govern species distributions. Following speciation, both intrinsic and extrinsic factors may determine how readily sympatry occurs. One possibility is that sympatry most readily occurs with ecological divergence, especially if broad-scale co-occurrence is mediated by niche differentiation. Time since divergence may also predict sympatry if hybridization and gene flow lead to the collapse of species boundaries between closely-related taxa. Here, we...

Data from: Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus

Therese A. Catanach, Andrew D. Sweet, Nam-Phuong D. Nguyen, Rhiannon M. Peery, Andrew H. Debevec, Andrea K. Thomer, Amanda C. Owings, Bret M. Boyd, Aron D. Katz, Felipe N. Soto-Adames & Julie M. Allen
Aligning sequences for phylogenetic analysis (multiple sequence alignment; MSA) is an important, but increasingly computationally expensive step with the recent surge in DNA sequence data. Much of this sequence data is publicly available, but can be extremely fragmentary (i.e., a combination of full genomes and genomic fragments), which can compound the computational issues related to MSA. Traditionally, alignments are produced with automated algorithms and then checked and/or corrected “by eye” prior to phylogenetic inference. However,...

Data from: From cacti to carnivores: improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales

Joseph Frederic Walker, Ya Yang, Tao Feng, Alfonso Timoneda, Jessica Mikenas, Vera Hutchison, Caroline Edwards, Ning Wang, Sonia Ahluwalia, Julia Olivieri, Nathanael Walker-Hale, Lucas C. Majure, Raúl Puente, Gudrun Kadereit, Maximillian Lauterbach, Urs Eggli, Hilda Flores-Olvera, Helga Ochoterena, Samuel F. Brockington, Michael J. Moore & Stephen A. Smith
Premise of the Study— The Caryophyllales contains ~12,500 species and is known for its cosmopolitan distribution, convergence of trait evolution, and extreme adaptations. Some relationships within the Caryophyllales, like those of many large plant clades, remain unclear and phylogenetic studies often recover alternative hypotheses. We explore the utility of broad and dense transcriptome sampling across the order for resolving evolutionary relationships in Caryophyllales. Methods— We generated 84 transcriptomes and combined these with 224 publicly available...

Data from: Rates of evolution: a quantitative synthesis

Philip D. Gingerich
One-generation step intervals, differences, and rates; longer base intervals, differences, and rates; and overlapping net intervals, differences, and rates for selection experiments (file 1: 15,431 rates), field studies (file 2: 12,461 rates), and fossil studies (file 3: 47,854 rates).

Registration Year

  • 2018

Resource Types

  • Dataset


  • University of Michigan-Ann Arbor
  • Yale University
  • University of Arizona
  • University of Pennsylvania
  • Stanford University
  • National Autonomous University of Mexico
  • University of Sao Paulo
  • Emory University
  • Rice University
  • University of Washington